AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i005_Pyrimidine_Biosynthesis_hpyl_reg_300.orf -o005_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP01209 157 AE000511 #2 RHP01210 111 AE000511 #3 RHP01211 72 AE000511 #4 RHP01212 53 AE000511 #5 RHP00334 98 AE000511 #6 RHP00335 143 AE000511 #7 RHP00488 66 AE000511 #8 RHP00630 300 AE000511 #9 RHP00632 78 AE000511 Motif number 1 ATTCATTAGCAATACTTTTAAGCAGAATATCT 1 62 1 AACTTTTAAG 0.926378 -96 ATTTAGCCAAAAACCATTTTGATCAAAGCTCT 2 43 1 AACATTTTGA 0.704024 -69 CATTTTGATCAAAGCTCTAAAATCAAGAGCAT 2 57 1 AACTCTAAAA 0.920262 -55 AAAAGCCTTTTTAAATCTTCTAAT 2 98 0 AACTTTTTAA 0.952135 -14 TTAACCCTCAAAGGTTTTTAAAACGC 3 5 0 AATTTTTAAA 0.701548 -68 TAAAATAGTAAAGATTTTAAAACTCAAAAAGG 3 44 1 AATTTTAAAA 0.821479 -29 TATCAATCCTTTTTGAGTTTTAAAAT 3 57 0 AACTTTTTGA 0.916682 -16 TCAATCCTTTTTCAAAAATAACCA 4 40 0 AACTTTTTCA 0.716123 -14 ACGCCACGCAAAAACCTAATAAAAAATACTTT 5 30 1 AACCTAATAA 0.845106 -69 CCTAATAAAAAATACTTTAAAATATTGATAAC 5 44 1 AACTTTAAAA 0.98422 -55 AACTAATCCTTAAAGAAAGAATGTAA 5 83 0 AACTTAAAGA 0.934287 -16 TACCAAACAAAACCCCCTAAAATTGAAATTGA 6 37 0 AACCCTAAAA 0.796891 -107 GGGATTTAAAAAGCTTAAAAAGAGTTTTCTA 8 10 1 AACTTAAAAA 0.962555 -291 GTGGCATTCAAACCCTTTAAAAAGGGTCTAGG 8 45 1 AACTTTAAAA 0.98422 -256 TAAAAACACGAATCCTTTTTGAAAATAAACTC 8 76 0 AACTTTTTGA 0.916682 -225 TAGAAATATGAAAACATAAAAACACGAATCCT 8 92 0 AACATAAAAA 0.847504 -209 CAGCATTTCAAACTCCTTATAGAAATATGAAA 8 111 0 AACCTTATAG 0.839439 -190 TTAAGCTTTAAACGCATAAAAGTTGCATTGAT 8 215 0 AACATAAAAG 0.686998 -86 TTATGCGTTTAAAGCTTAAAAACTTTAAGTCT 8 228 1 AACTTAAAAA 0.962555 -73 AACTACCCTAAAATCTTTATGGGTAAAATGC 8 280 1 AACTTTATGG 0.894803 -21 ATTAATTCTTTAAAAAGCGTTTTAT 9 4 1 AACTTTAAAA 0.98422 -75 ** ******** Masking position 2 Map Score: 28.2043 Number of sites scoring better than the average of aligned sites = 2498 Number in coding regions = 2137 Number in noncoding regions = 361 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 2 ATATTTTCACTAAAATAATATTGAAAGAATTTAATC 1 23 0 TAAAATAAAA 0.983911 -135 GAAACAAGCTTATAATAAAAATGAAATTTAAATTTT 1 94 0 TATAATAAAA 0.90794 -64 ATCAAAGCTCTAAAATCAAGAGCATAGAAAATTTAT 2 64 1 TAAAATCATA 0.880251 -48 AAAAGCCTTTTTAAATCTTCTAATAAATTTTCTATG 2 86 0 TTAAATCTAA 0.64776 -26 CTTTGAGGGTTAAAATAGTGTAAAATAGTAAAGATT 3 24 1 TAAAATAAAT 0.938332 -49 TTTGTTATCCTAAAAAAGACAAGAAATGGTTATTTT 4 14 1 TAAAAAAAAA 0.938332 -40 AAAAACCTAATAAAAAATACTTTAAAATATTGATAA 5 39 1 TAAAAAAAAA 0.937923 -60 CAAAATGTAGTAAAATACCAAACAAAACCCCCTAAA 6 48 0 TAAAATAAAA 0.983918 -96 CTAGGTCCAATATAATAGCGCAAAATGTAGTAAAAT 6 68 0 TATAATAAAT 0.710668 -76 TTAGCTAAAATAAAATCTATATTATAACTAAAAGGG 7 35 1 TAAAATCATA 0.691741 -32 GGGATTTAAAAAGCTTAAAAAGAGTTTTCTA 8 6 1 TTAAAAAAAA 0.710642 -295 CATTGATTGGTAAAATCATGTTATAACAATGTTCTA 8 186 0 TAAAATCTAA 0.918019 -115 TAGTTTAACCTAAAATCTCTAATTAAGACTTAAAGT 8 249 0 TAAAATCTAA 0.912046 -52 GATTTTAGGTTAAACTACCCTAAAATCTTTATGGGT 8 268 1 TAAACTAAAT 0.658662 -33 TAAAAAACGATAAAATACACTCTAAAAATAAATAAA 9 37 1 TAAAATAAAA 0.98391 -42 TAAAAATAAATAAAATATGCGAGAAAAATC 9 59 1 TAAAATAAAA 0.983919 -20 ******* *** Masking position 4 Map Score: 20.6216 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 570 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 3 ATACAAAATTTTGATAATGGCTGGTGTTTG 1 129 0 TTGATAATGG 0.72802 -29 TAGAGCTTTGATCAAAATGGTTTTTGGCTA 2 46 0 ATCAAAATGG 0.73432 -66 TATTAGAAGATTTAAAAAGGCTTTT 2 97 1 TTTAAAAAGG 0.821841 -15 GATTTTAAAACTCAAAAAGGATTGATA 3 56 1 CTCAAAAAGG 0.967118 -17 TTTTGTTATCCTAAAAAAGACAAGAAATGG 4 13 1 CTAAAAAAGA 0.72656 -41 ATGGTTATTTTTGAAAAAGGATTGA 4 39 1 TTGAAAAAGG 0.948261 -15 AAATTGAAGTCTGAAAATAGGATAATAGTT 6 14 0 CTGAAAATAG 0.757962 -130 TTTATTTTAGCTAAAAATGGCATGGGTTTT 7 19 0 CTAAAAATGG 0.975319 -48 TATATTATAACTAAAAGGGGGTTTT 7 52 1 CTAAAAGGGG 0.931779 -15 TTTAAAAAGCTTAAAAAGAGTTTTCTAATA 8 15 1 TTAAAAAGAG 0.800447 -286 AAAGAGTTTTCTAATAGTGGCATTCAAACC 8 29 1 CTAATAGTGG 0.648031 -272 TTCAAACCCTTTAAAAAGGGTCTAGGAGTT 8 51 1 TTAAAAAGGG 0.969422 -250 GGAGTTTATTTTCAAAAAGGATTCGTGTTT 8 75 1 TTCAAAAAGG 0.948261 -226 ATTAATTCTTTAAAAAGCGTTTTATCTAA 9 10 1 TTAAAAAGCG 0.8612 -69 AGCGTTTTATCTAAAAAACGATAAAATACA 9 26 1 CTAAAAAACG 0.90187 -53 ********** Masking position 6 Map Score: 16.2607 Number of sites scoring better than the average of aligned sites = 1165 Number in coding regions = 964 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 4 TTTCACTAAAATAATATTGAAAGAATTTAA 1 25 0 ATAATATTGA 0.884469 -133 CAGAATATCTAAAATTTAAATTTCATTTTT 1 84 1 AAAATTTAAA 0.914639 -74 ATTATAATACAAAATTTTGATAATGGCTGG 1 135 0 AAAATTTTGA 0.94443 -23 AAAATAGTGTAAAATAGTAAAGATTTTAAA 3 35 1 AAAATAGTAA 0.87088 -38 AAAATACTTTAAAATATTGATAACGCTTCG 5 52 1 AAAATATTGA 0.944403 -47 AAAACCCCCTAAAATTGAAATTGAAGTCTG 6 31 0 AAAATTGAAA 0.82166 -113 AACTCAATAAATAATTTTAATTAACCCTAC 6 106 0 ATAATTTTAA 0.876382 -38 CCTTTTAGTTATAATATAGATTTTATTTTA 7 40 0 ATAATATAGA 0.840151 -27 TAGAAATATGAAAACATAAAAACACGAATC 8 94 0 AAAACATAAA 0.821659 -207 TTAAAGCTTAAAAACTTTAAGTCTTAATTA 8 236 1 AAAACTTTAA 0.870887 -65 ********** Masking position 4 Map Score: 7.21176 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 405 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 5 CCCTCAAAGGTTTTTAAAACGC 3 1 0 TTTAAAACGC 0.984022 -72 AATAGTAAAGATTTTAAAACTCAAAAAGGATT 3 47 1 ATTAAAACTC 0.939912 -26 TACTTTAAAATATTGATAACGCTTCGTTTACA 5 56 1 TTGATAACGC 0.825954 -43 TCCTTGCTAAAACCCATGCCATTTT 7 4 1 TGTAAAACCC 0.976439 -63 CTTTTTAAGCTTTTTAAATCCC 8 1 0 TTTAAATCCC 0.835379 -300 GAATGCCACTATTAGAAAACTCTTTTTAAGCT 8 22 0 ATGAAAACTC 0.88434 -279 GACAAAACAAAAGGTAAAACTCCTAGAACATT 8 163 1 AGTAAAACTC 0.952686 -138 AAAATCTTTATGGGTAAAATGC 8 289 1 TGTAAAATGC 0.886018 -12 TATCGTTTTTTAGATAAAACGCTTTTTAAAGA 9 17 0 TGTAAAACGC 0.987514 -62 * * ******** Masking position 6 Map Score: 6.08465 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 467 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 TCTCATTCATGCTCCATGACGATC 2 5 0 GCTCCATGAC 0.947535 -107 GTTTTACTCCTTGAATTCAACTCAA 6 129 0 ACTCCTTGAA 0.967329 -15 TTGAAAATAAACTCCTAGACCCTTTTTAAA 8 60 0 ACTCCTAGAC 0.988619 -241 AAATGCTGAAGCTTCTAGAATGATTCTAGA 8 135 1 GCTTCTAGAA 0.967053 -166 CTTCTAGAATGATTCTAGACAAAACAAAAG 8 146 1 GATTCTAGAC 0.87715 -155 AAAAGGTAAAACTCCTAGAACATTGTTATA 8 171 1 ACTCCTAGAA 0.98222 -130 ********** Masking position 3 Map Score: 5.15196 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 29 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 ATATTTTCACTAAAATAATATTGAAAGAAT 1 29 0 TAAAATAATA 0.783964 -129 ATTATTTTAGTGAAAATATATGATTCATTA 1 40 1 TGAAAATATA 0.92133 -118 AAGCTTATAATAAAAATGAAATTTAAATTT 1 95 0 TAAAAATGAA 0.852043 -63 TAAAATAGTGTAAAATAGTAAAGATTTTAA 3 34 1 TAAAATAGTA 0.772406 -39 TGGTTATTTTTGAAAAAGGATTGA 4 40 1 TGAAAAAGGA 0.800203 -14 TTTGAAAAAATAGGGGGGGACG 5 3 1 TGAAAAAATA 0.921336 -96 CCCCTAAAATTGAAATTGAAGTCTGAAAAT 6 26 0 TGAAATTGAA 0.865907 -118 CATTTTTAGCTAAAATAAAATCTATATTAT 7 30 1 TAAAATAAAA 0.784049 -37 GAATCCTTTTTGAAAATAAACTCCTAGACC 8 69 0 TGAAAATAAA 0.921336 -232 TATAGAAATATGAAAACATAAAAACACGAA 8 96 0 TGAAAACATA 0.810699 -205 AAATACACTCTAAAAATAAATAAAATATGC 9 49 1 TAAAAATAAA 0.860291 -30 ********** Masking position 5 Map Score: 8.8432 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 552 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 ********** No masking Map Score: -1.4826e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ********** No masking Map Score: -1.4826e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: -1.4826e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0